Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:54:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tik_25912/11_2022/7tik_25912.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 2565 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "B" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "C" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain: "D" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "E" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "F" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 319 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Time building chain proxies: 2.15, per 1000 atoms: 0.84 Number of scatterers: 2565 At special positions: 0 Unit cell: (52, 42.25, 118.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 531 8.00 N 450 7.00 C 1584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 370.8 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 918 through 988 Processing helix chain 'B' and resid 919 through 988 Processing helix chain 'C' and resid 919 through 988 Processing helix chain 'D' and resid 1179 through 1193 Processing helix chain 'D' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU D1197 " --> pdb=" O ASN D1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1194 through 1197' Processing helix chain 'E' and resid 1179 through 1193 Processing helix chain 'E' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU E1197 " --> pdb=" O ASN E1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1194 through 1197' Processing helix chain 'F' and resid 1179 through 1193 Processing helix chain 'F' and resid 1194 through 1197 removed outlier: 3.618A pdb=" N LEU F1197 " --> pdb=" O ASN F1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1194 through 1197' 232 hydrogen bonds defined for protein. 696 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 480 1.29 - 1.35: 420 1.35 - 1.41: 89 1.41 - 1.48: 382 1.48 - 1.54: 1206 Bond restraints: 2577 Sorted by residual: bond pdb=" CA LEU C 966 " pdb=" C LEU C 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.44e-01 bond pdb=" CA LEU B 966 " pdb=" C LEU B 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" CB ASN C 955 " pdb=" CG ASN C 955 " ideal model delta sigma weight residual 1.516 1.494 0.022 2.50e-02 1.60e+03 8.08e-01 bond pdb=" CA LEU A 966 " pdb=" C LEU A 966 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.29e-02 6.01e+03 8.00e-01 bond pdb=" CA LEU B 962 " pdb=" C LEU B 962 " ideal model delta sigma weight residual 1.524 1.512 0.011 1.29e-02 6.01e+03 7.82e-01 ... (remaining 2572 not shown) Histogram of bond angle deviations from ideal: 103.19 - 108.80: 64 108.80 - 114.42: 1608 114.42 - 120.03: 744 120.03 - 125.65: 1052 125.65 - 131.27: 9 Bond angle restraints: 3477 Sorted by residual: angle pdb=" CA ILE B 980 " pdb=" CB ILE B 980 " pdb=" CG1 ILE B 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.59e+00 angle pdb=" CA ILE A 980 " pdb=" CB ILE A 980 " pdb=" CG1 ILE A 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" CA ILE C 980 " pdb=" CB ILE C 980 " pdb=" CG1 ILE C 980 " ideal model delta sigma weight residual 110.40 115.66 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" C ASP C 979 " pdb=" N ILE C 980 " pdb=" CA ILE C 980 " ideal model delta sigma weight residual 120.64 115.62 5.02 1.64e+00 3.72e-01 9.39e+00 angle pdb=" C ASP B 979 " pdb=" N ILE B 980 " pdb=" CA ILE B 980 " ideal model delta sigma weight residual 120.64 115.64 5.00 1.64e+00 3.72e-01 9.29e+00 ... (remaining 3472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1404 17.40 - 34.81: 159 34.81 - 52.21: 21 52.21 - 69.61: 12 69.61 - 87.02: 6 Dihedral angle restraints: 1602 sinusoidal: 621 harmonic: 981 Sorted by residual: dihedral pdb=" CA ASN F1192 " pdb=" CB ASN F1192 " pdb=" CG ASN F1192 " pdb=" OD1 ASN F1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.29 -71.71 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN D1192 " pdb=" CB ASN D1192 " pdb=" CG ASN D1192 " pdb=" OD1 ASN D1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.31 -71.69 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASN E1192 " pdb=" CB ASN E1192 " pdb=" CG ASN E1192 " pdb=" OD1 ASN E1192 " ideal model delta sinusoidal sigma weight residual 120.00 -168.33 -71.67 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 1599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 210 0.028 - 0.056: 165 0.056 - 0.084: 33 0.084 - 0.112: 7 0.112 - 0.140: 17 Chirality restraints: 432 Sorted by residual: chirality pdb=" CB ILE B 980 " pdb=" CA ILE B 980 " pdb=" CG1 ILE B 980 " pdb=" CG2 ILE B 980 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CB ILE A 980 " pdb=" CA ILE A 980 " pdb=" CG1 ILE A 980 " pdb=" CG2 ILE A 980 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA VAL E1176 " pdb=" N VAL E1176 " pdb=" C VAL E1176 " pdb=" CB VAL E1176 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 429 not shown) Planarity restraints: 456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 981 " 0.007 2.00e-02 2.50e+03 9.97e-03 1.74e+00 pdb=" CG PHE A 981 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 981 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 981 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 981 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 981 " -0.007 2.00e-02 2.50e+03 9.81e-03 1.68e+00 pdb=" CG PHE B 981 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 981 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 981 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 981 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 981 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 981 " -0.007 2.00e-02 2.50e+03 9.74e-03 1.66e+00 pdb=" CG PHE C 981 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 981 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 981 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 981 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 981 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 981 " -0.000 2.00e-02 2.50e+03 ... (remaining 453 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 463 2.75 - 3.29: 2698 3.29 - 3.83: 4418 3.83 - 4.36: 4841 4.36 - 4.90: 8357 Nonbonded interactions: 20777 Sorted by model distance: nonbonded pdb=" OG SER A 943 " pdb=" OE2 GLU F1182 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP A 936 " pdb=" NH2 ARG F1185 " model vdw 2.259 2.520 nonbonded pdb=" O LYS B 964 " pdb=" OG SER B 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS A 964 " pdb=" OG SER A 967 " model vdw 2.283 2.440 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.283 2.440 ... (remaining 20772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1584 2.51 5 N 450 2.21 5 O 531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.450 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.027 2577 Z= 0.418 Angle : 0.491 5.265 3477 Z= 0.283 Chirality : 0.042 0.140 432 Planarity : 0.003 0.016 456 Dihedral : 16.305 87.018 954 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.41), residues: 327 helix: 1.84 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -2.67 (0.54), residues: 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.312 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.5683 time to fit residues: 32.3136 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN B 960 ASN C 960 ASN D1192 ASN E1192 ASN F1192 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2577 Z= 0.183 Angle : 0.390 6.926 3477 Z= 0.209 Chirality : 0.037 0.137 432 Planarity : 0.002 0.011 456 Dihedral : 3.311 12.742 339 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.47 (0.44), residues: 327 helix: 3.99 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -1.09 (0.68), residues: 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.263 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.5939 time to fit residues: 32.4105 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 20.0000 chunk 10 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 2577 Z= 0.193 Angle : 0.372 5.432 3477 Z= 0.200 Chirality : 0.037 0.131 432 Planarity : 0.002 0.011 456 Dihedral : 3.033 12.048 339 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.24 (0.45), residues: 327 helix: 4.56 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.87 (0.71), residues: 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.306 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.5870 time to fit residues: 31.4797 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.0799 time to fit residues: 0.5295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 978 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2577 Z= 0.222 Angle : 0.371 4.564 3477 Z= 0.209 Chirality : 0.037 0.136 432 Planarity : 0.002 0.015 456 Dihedral : 3.082 11.550 339 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.33 (0.45), residues: 327 helix: 4.59 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.70 (0.74), residues: 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.295 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.5555 time to fit residues: 29.8173 Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.6860 time to fit residues: 1.8388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2577 Z= 0.212 Angle : 0.404 5.529 3477 Z= 0.222 Chirality : 0.037 0.131 432 Planarity : 0.002 0.025 456 Dihedral : 3.078 11.082 339 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.38 (0.45), residues: 327 helix: 4.60 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.58 (0.75), residues: 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.300 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.5719 time to fit residues: 31.3115 Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2577 Z= 0.192 Angle : 0.384 5.707 3477 Z= 0.221 Chirality : 0.038 0.144 432 Planarity : 0.002 0.029 456 Dihedral : 3.085 10.809 339 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.51 (0.45), residues: 327 helix: 4.68 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.49 (0.75), residues: 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.298 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.5702 time to fit residues: 30.0136 Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.311 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.7494 time to fit residues: 1.9583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.021 2577 Z= 0.218 Angle : 0.420 6.278 3477 Z= 0.230 Chirality : 0.038 0.155 432 Planarity : 0.002 0.026 456 Dihedral : 3.115 11.415 339 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.45), residues: 327 helix: 4.66 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.36 (0.77), residues: 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.308 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.5942 time to fit residues: 31.2588 Evaluate side-chains 50 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.4473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 chunk 30 optimal weight: 0.0030 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 2577 Z= 0.157 Angle : 0.390 6.338 3477 Z= 0.224 Chirality : 0.037 0.166 432 Planarity : 0.002 0.027 456 Dihedral : 3.018 12.044 339 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.79 (0.45), residues: 327 helix: 4.84 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.22 (0.78), residues: 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.318 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.5569 time to fit residues: 28.7516 Evaluate side-chains 50 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.4488 time to fit residues: 1.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN E1159 HIS F1159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 2577 Z= 0.252 Angle : 0.441 6.185 3477 Z= 0.248 Chirality : 0.039 0.160 432 Planarity : 0.002 0.027 456 Dihedral : 3.184 13.803 339 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.59 (0.45), residues: 327 helix: 4.69 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.27 (0.78), residues: 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.315 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.5923 time to fit residues: 31.7506 Evaluate side-chains 50 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 2577 Z= 0.232 Angle : 0.464 6.847 3477 Z= 0.261 Chirality : 0.039 0.155 432 Planarity : 0.002 0.027 456 Dihedral : 3.197 14.355 339 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.46 (0.45), residues: 327 helix: 4.57 (0.27), residues: 252 sheet: None (None), residues: 0 loop : -0.21 (0.79), residues: 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.265 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 0.5941 time to fit residues: 30.5146 Evaluate side-chains 48 residues out of total 297 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.143377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.121524 restraints weight = 3542.923| |-----------------------------------------------------------------------------| r_work (start): 0.4086 rms_B_bonded: 2.07 r_work: 0.4070 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.4056 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work: 0.4041 rms_B_bonded: 1.95 restraints_weight: 0.1250 r_work: 0.4026 rms_B_bonded: 2.07 restraints_weight: 0.0625 r_work: 0.4010 rms_B_bonded: 2.23 restraints_weight: 0.0312 r_work: 0.3992 rms_B_bonded: 2.44 restraints_weight: 0.0156 r_work: 0.3973 rms_B_bonded: 2.68 restraints_weight: 0.0078 r_work: 0.3951 rms_B_bonded: 2.98 restraints_weight: 0.0039 r_work: 0.3927 rms_B_bonded: 3.32 restraints_weight: 0.0020 r_work: 0.3901 rms_B_bonded: 3.72 restraints_weight: 0.0010 r_work: 0.3872 rms_B_bonded: 4.18 restraints_weight: 0.0005 r_work: 0.3838 rms_B_bonded: 4.72 restraints_weight: 0.0002 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2577 Z= 0.228 Angle : 0.441 6.331 3477 Z= 0.254 Chirality : 0.039 0.159 432 Planarity : 0.002 0.029 456 Dihedral : 3.193 14.260 339 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.45), residues: 327 helix: 4.59 (0.28), residues: 252 sheet: None (None), residues: 0 loop : -0.16 (0.79), residues: 75 =============================================================================== Job complete usr+sys time: 1156.25 seconds wall clock time: 22 minutes 13.62 seconds (1333.62 seconds total)